1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Alam, S.L.
Sun, J.
Payne, M.
Welch, B.D.
Blake, B.K.
Davis, D.R.
Meyer, H.H.
Emr, S.D.
Sundquist, W.I.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
Zn 2
65.409
ZINC ION
non-polymer
UK
Embo J.
EMJODG
0897
0261-4189
23
1411
1421
10.1038/sj.emboj.7600114
15029239
Ubiquitin interactions of NZF zinc fingers.
2004
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
278
20225
20234
10.1074/jbc.M300459200
Structure and ubiquitin interactions of the conserved zinc finger domain of Npl4.
2003
10.2210/pdb1q5w/pdb
pdb_00001q5w
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
3376.865
homolog of yeast nuclear protein localization 4
Npl4 NZF domain (residues 580-608)
1
man
polymer
8576.831
Ubiquitin
1
man
polymer
65.409
ZINC ION
1
syn
non-polymer
no
no
GSTSAMWACQHCTFMNQPGTGHCEMCSLPRT
GSTSAMWACQHCTFMNQPGTGHCEMCSLPRT
A
polypeptide(L)
no
no
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
B
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Norway rat
Rattus
Escherichia
Escherichia coli
sample
NPL4
10116
Rattus norvegicus
469008
Escherichia coli BL21(DE3)
BL21(DE3)
T7
pGEX2T
human
Homo
Escherichia
Escherichia coli
sample
(UBA52 OR UBCEP2) AND UBB AND UBC AND (UBA80 OR UBCEP1 OR RPS27A)
9606
Homo sapiens
469008
Escherichia coli BL21(DE3)
BL21(DE3)
T7
pET3d
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_conn_angle
pdbx_struct_oper_list
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2004-03-30
1
1
2008-04-29
1
2
2011-07-13
1
3
2022-03-02
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Npl4 Zinc finger structure
RCSB
Y
RCSB
2003-08-11
REL
ZN
ZINC ION
inter-molecular NOEs identified with half-filtered and double half-filtered NOE experiments and samples #1 and #2.
structures with the least restraint violations,structures with the lowest energy,target function
200
20
3D_13C-separated_NOESY
3D_15N-separated_NOESY
HNCACB, CBCACONH, CCONH, HCCONH,HNCO, HNCACO
3D_13C-separated_NOESY
3D_15N-separated_NOESY
HNCACB, CBCACONH, CCONH, HCCONH,HNCO, HNCACO
70mM
5.5
ambient
291
K
70mM
5.5
ambient
291
K
70mM
5.5
ambient
291
K
70mM
5.5
ambient
291
K
structures are based on 2072 NOE-derived
distance constraints, 145 dihedral angle constraints ,104 H-Bond constraints, and 14 Zinc-coordination constraints.
Torsion angle dynamics followed by simulated annealing
1
fewest violations,lowest energy
1mM Npl4 NZF U-15N,13C; 2mM unlabeled-Ubiquitin; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10%
90% H2O/10% D2O
1mM Ubiquitin U-15N,13C; 2mM unlabeled-Npl4 NZF; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10%
90% H2O/10% D2O
1mM Ubiquitin U-15N; 2mM unlabeled-Npl4 NZF; 20mM phosphate buffer pH 5.5, 50mM
90% H2O/10% D2O
1mM Npl4 NZF U-15N; 2mM unlabeled-Ubiquitin; 20mM phosphate buffer pH 5.5, 50mM NaCl; 90% H2O, 10%
90% H2O/10% D2O
Peter Guntert
refinement
DYANA
1.5
"CRYSTALLOGRAPHY AND NMR SYSTEM (CNS): A NEW SOFTWARE SYSTEM
refinement
CNS
1.1
www.accelrys.com
processing
Felix
97
T.D. Goddard and D.G. Kneller, SPARKY 3,
data analysis
Sparky
3.106
600
Varian
INOVA
ZN2
32
3
ZN
ZN
32
A
GLY
1
n
1
GLY
1
A
SER
2
n
2
SER
2
A
THR
3
n
3
THR
3
A
SER
4
n
4
SER
4
A
ALA
5
n
5
ALA
5
A
MET
6
n
6
MET
6
A
TRP
7
n
7
TRP
7
A
ALA
8
n
8
ALA
8
A
CYS
9
n
9
CYS
9
A
GLN
10
n
10
GLN
10
A
HIS
11
n
11
HIS
11
A
CYS
12
n
12
CYS
12
A
THR
13
n
13
THR
13
A
PHE
14
n
14
PHE
14
A
MET
15
n
15
MET
15
A
ASN
16
n
16
ASN
16
A
GLN
17
n
17
GLN
17
A
PRO
18
n
18
PRO
18
A
GLY
19
n
19
GLY
19
A
THR
20
n
20
THR
20
A
GLY
21
n
21
GLY
21
A
HIS
22
n
22
HIS
22
A
CYS
23
n
23
CYS
23
A
GLU
24
n
24
GLU
24
A
MET
25
n
25
MET
25
A
CYS
26
n
26
CYS
26
A
SER
27
n
27
SER
27
A
LEU
28
n
28
LEU
28
A
PRO
29
n
29
PRO
29
A
ARG
30
n
30
ARG
30
A
THR
31
n
31
THR
31
A
MET
101
n
1
MET
101
B
GLN
102
n
2
GLN
102
B
ILE
103
n
3
ILE
103
B
PHE
104
n
4
PHE
104
B
VAL
105
n
5
VAL
105
B
LYS
106
n
6
LYS
106
B
THR
107
n
7
THR
107
B
LEU
108
n
8
LEU
108
B
THR
109
n
9
THR
109
B
GLY
110
n
10
GLY
110
B
LYS
111
n
11
LYS
111
B
THR
112
n
12
THR
112
B
ILE
113
n
13
ILE
113
B
THR
114
n
14
THR
114
B
LEU
115
n
15
LEU
115
B
GLU
116
n
16
GLU
116
B
VAL
117
n
17
VAL
117
B
GLU
118
n
18
GLU
118
B
PRO
119
n
19
PRO
119
B
SER
120
n
20
SER
120
B
ASP
121
n
21
ASP
121
B
THR
122
n
22
THR
122
B
ILE
123
n
23
ILE
123
B
GLU
124
n
24
GLU
124
B
ASN
125
n
25
ASN
125
B
VAL
126
n
26
VAL
126
B
LYS
127
n
27
LYS
127
B
ALA
128
n
28
ALA
128
B
LYS
129
n
29
LYS
129
B
ILE
130
n
30
ILE
130
B
GLN
131
n
31
GLN
131
B
ASP
132
n
32
ASP
132
B
LYS
133
n
33
LYS
133
B
GLU
134
n
34
GLU
134
B
GLY
135
n
35
GLY
135
B
ILE
136
n
36
ILE
136
B
PRO
137
n
37
PRO
137
B
PRO
138
n
38
PRO
138
B
ASP
139
n
39
ASP
139
B
GLN
140
n
40
GLN
140
B
GLN
141
n
41
GLN
141
B
ARG
142
n
42
ARG
142
B
LEU
143
n
43
LEU
143
B
ILE
144
n
44
ILE
144
B
PHE
145
n
45
PHE
145
B
ALA
146
n
46
ALA
146
B
GLY
147
n
47
GLY
147
B
LYS
148
n
48
LYS
148
B
GLN
149
n
49
GLN
149
B
LEU
150
n
50
LEU
150
B
GLU
151
n
51
GLU
151
B
ASP
152
n
52
ASP
152
B
GLY
153
n
53
GLY
153
B
ARG
154
n
54
ARG
154
B
THR
155
n
55
THR
155
B
LEU
156
n
56
LEU
156
B
SER
157
n
57
SER
157
B
ASP
158
n
58
ASP
158
B
TYR
159
n
59
TYR
159
B
ASN
160
n
60
ASN
160
B
ILE
161
n
61
ILE
161
B
GLN
162
n
62
GLN
162
B
LYS
163
n
63
LYS
163
B
GLU
164
n
64
GLU
164
B
SER
165
n
65
SER
165
B
THR
166
n
66
THR
166
B
LEU
167
n
67
LEU
167
B
HIS
168
n
68
HIS
168
B
LEU
169
n
69
LEU
169
B
VAL
170
n
70
VAL
170
B
LEU
171
n
71
LEU
171
B
ARG
172
n
72
ARG
172
B
LEU
173
n
73
LEU
173
B
ARG
174
n
74
ARG
174
B
GLY
175
n
75
GLY
175
B
GLY
176
n
76
GLY
176
B
author_defined_assembly
2
dimeric
A
CYS
9
A
SG
CYS
9
1_555
A
ZN
32
C
ZN
ZN
1_555
A
CYS
12
A
SG
CYS
12
1_555
107.4
A
CYS
9
A
SG
CYS
9
1_555
A
ZN
32
C
ZN
ZN
1_555
A
CYS
23
A
SG
CYS
23
1_555
104.2
A
CYS
12
A
SG
CYS
12
1_555
A
ZN
32
C
ZN
ZN
1_555
A
CYS
23
A
SG
CYS
23
1_555
113.0
A
CYS
9
A
SG
CYS
9
1_555
A
ZN
32
C
ZN
ZN
1_555
A
CYS
26
A
SG
CYS
26
1_555
103.7
A
CYS
12
A
SG
CYS
12
1_555
A
ZN
32
C
ZN
ZN
1_555
A
CYS
26
A
SG
CYS
26
1_555
124.8
A
CYS
23
A
SG
CYS
23
1_555
A
ZN
32
C
ZN
ZN
1_555
A
CYS
26
A
SG
CYS
26
1_555
101.7
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
TRP
7
A
N
TRP
7
A
O
ASN
16
A
O
ASN
16
B
O
ILE
113
B
O
ILE
13
B
N
VAL
105
B
N
VAL
5
B
N
PHE
104
B
N
PHE
4
B
O
LEU
167
B
O
LEU
67
B
O
HIS
168
B
O
HIS
68
B
N
ILE
144
B
N
ILE
44
4
A
A
H
O
CYS
LEU
23
28
1.59
7
A
A
H
O
CYS
LEU
23
28
1.59
7
A
A
H
O
CYS
PHE
9
14
1.59
9
A
A
H
O
CYS
LEU
23
28
1.59
10
A
A
H
O
CYS
PHE
9
14
1.58
12
A
A
H
O
CYS
LEU
23
28
1.57
14
A
A
H
O
CYS
LEU
23
28
1.58
18
B
B
H
O
VAL
ILE
105
113
1.58
1
A
SER
4
-65.56
-170.19
1
A
CYS
9
-46.57
157.59
1
A
HIS
11
-131.99
-57.86
1
A
THR
13
81.06
23.53
1
B
ASP
121
-63.98
-167.62
1
B
ASN
160
86.63
44.04
2
A
SER
2
-176.64
144.16
2
A
THR
3
-98.90
31.60
2
A
ALA
5
-177.63
122.90
2
A
CYS
9
-47.57
157.21
2
A
HIS
11
-132.31
-57.81
2
B
ASP
121
-61.92
-165.12
2
B
ASN
160
85.74
51.46
2
B
SER
165
-59.00
173.30
2
B
ARG
174
46.24
-169.16
3
A
THR
3
-176.71
102.41
3
A
ALA
5
62.07
-176.23
3
A
CYS
9
-46.79
157.45
3
A
HIS
11
-137.81
-54.11
3
A
THR
13
54.77
74.19
3
B
ASP
121
-65.29
-168.07
3
B
ALA
146
39.13
41.69
3
B
ASN
160
83.89
50.47
4
A
SER
2
-176.42
-40.43
4
A
ALA
5
-92.62
50.85
4
A
CYS
9
-48.64
157.41
4
A
HIS
11
-130.73
-57.37
4
A
MET
25
-123.02
-58.92
4
B
ASP
121
-64.37
-167.66
4
B
ASN
160
84.29
49.72
5
A
SER
2
60.83
102.56
5
A
SER
4
-127.99
-74.81
5
A
ALA
5
-166.36
50.30
5
A
CYS
9
-47.78
157.45
5
A
HIS
11
-135.25
-55.89
5
A
MET
25
-123.04
-59.65
5
B
ASP
121
-58.09
-165.60
5
B
ASN
160
86.59
50.62
5
B
SER
165
-58.58
171.96
6
A
SER
2
-161.90
106.58
6
A
THR
3
60.36
155.62
6
A
CYS
9
-47.22
157.19
6
A
HIS
11
-137.53
-56.80
6
B
ASP
121
-60.31
-165.28
6
B
ASN
160
86.77
50.17
7
A
SER
2
61.62
113.79
7
A
THR
3
-163.75
-69.36
7
A
ALA
5
-176.82
124.54
7
A
CYS
9
-46.40
157.41
7
A
HIS
11
-130.21
-54.36
7
B
ASP
121
-58.98
-165.80
7
B
ASN
160
83.26
48.79
7
B
SER
165
-59.19
172.98
7
B
ARG
174
-59.59
172.99
8
A
SER
2
-60.38
-176.22
8
A
THR
3
-99.00
31.76
8
A
CYS
9
-48.21
156.81
8
A
HIS
11
-135.88
-56.44
8
A
MET
25
-123.13
-60.67
8
B
ASP
121
-60.26
-166.61
8
B
ASN
160
87.42
48.35
8
B
LEU
173
-68.14
-173.94
9
A
SER
2
-176.72
-40.33
9
A
ALA
5
-92.08
50.50
9
A
CYS
9
-48.23
157.54
9
A
HIS
11
-128.03
-57.60
9
B
ASP
121
-60.68
-165.77
9
B
ASN
160
82.91
52.44
10
A
THR
3
-171.86
100.01
10
A
ALA
5
75.84
48.82
10
A
CYS
9
-48.05
157.83
10
A
HIS
11
-131.19
-54.55
10
A
MET
25
-123.13
-59.47
10
B
ASP
121
-60.49
-164.91
10
B
ASN
160
83.18
49.24
10
B
ARG
174
59.32
165.63
11
A
THR
3
-172.44
129.84
11
A
SER
4
-130.36
-68.39
11
A
ALA
5
-160.50
52.05
11
A
CYS
9
-46.84
157.51
11
A
HIS
11
-135.05
-53.49
11
A
THR
13
54.50
74.45
11
A
MET
25
-123.09
-61.00
11
B
ASP
121
-59.51
-167.90
11
B
ALA
146
39.39
41.33
11
B
ASN
160
83.48
52.86
12
A
SER
2
68.00
-71.24
12
A
THR
3
60.30
79.93
12
A
SER
4
-98.05
-67.26
12
A
ALA
5
61.00
-176.22
12
A
CYS
9
-42.92
157.00
12
A
HIS
11
-135.35
-53.75
12
A
THR
13
53.42
74.19
12
A
MET
25
-120.24
-59.97
12
B
ASP
121
-60.47
-165.21
12
B
ASN
160
83.21
54.04
13
A
CYS
9
-46.21
157.17
13
A
HIS
11
-138.85
-52.77
13
A
MET
25
-123.03
-61.62
13
B
ASP
121
-58.11
-165.93
13
B
ASN
160
81.89
56.52
14
A
CYS
9
-46.71
157.11
14
A
HIS
11
-133.60
-53.17
14
A
THR
13
56.13
73.32
14
A
MET
25
-123.11
-61.01
14
A
SER
27
80.23
14.91
14
B
ASP
121
-59.77
-165.60
14
B
ASN
160
84.11
51.85
15
A
SER
2
60.50
-178.92
15
A
CYS
9
-47.19
157.47
15
B
ASP
121
-57.84
-169.39
15
B
ASN
160
83.33
54.43
15
B
SER
165
-58.34
172.28
16
A
SER
2
60.19
158.64
16
A
SER
4
60.10
-171.13
16
A
CYS
9
-47.92
157.42
16
A
THR
13
53.73
76.39
16
A
MET
25
-122.40
-60.31
16
B
ASP
121
-60.60
-167.63
16
B
ALA
146
39.24
41.22
16
B
ASN
160
85.27
50.37
17
A
SER
2
-131.68
-68.14
17
A
THR
3
61.57
114.10
17
A
SER
4
60.82
-172.77
17
A
CYS
9
-47.46
156.81
17
A
THR
13
53.45
77.07
17
A
MET
25
-123.05
-60.84
17
B
ASP
121
-59.20
-167.52
17
B
ALA
146
38.37
41.30
17
B
ASN
160
85.71
51.56
17
B
SER
165
-57.81
172.95
18
A
SER
4
60.23
83.29
18
A
CYS
9
-46.61
157.33
18
A
HIS
11
-137.28
-55.36
18
A
THR
13
51.11
73.06
18
A
MET
25
-122.98
-61.80
18
B
ASP
121
-61.09
-167.84
18
B
ALA
146
37.78
41.25
18
B
ASN
160
82.08
53.75
19
A
CYS
9
-45.71
156.78
19
A
HIS
11
-144.49
-55.30
19
A
MET
25
-123.13
-59.12
19
B
ASP
121
-59.69
-167.11
19
B
ALA
146
36.70
43.49
19
B
ASN
160
88.43
47.58
20
A
SER
2
-173.37
36.29
20
A
SER
4
-60.40
-170.09
20
A
ALA
5
-94.49
50.78
20
A
CYS
9
-46.43
157.54
20
A
HIS
11
-137.82
-56.30
20
A
MET
25
-120.19
-59.11
20
B
ASP
121
-60.33
-166.09
20
B
ASN
160
85.43
50.49
20
B
SER
165
-56.11
172.03
Ubiquitin Recognition by Npl4 Zinc-Fingers
1
N
N
2
N
N
3
N
N
B
THR
122
B
THR
22
HELX_P
B
GLU
134
B
GLU
34
1
1
13
metalc
2.376
A
CYS
9
A
SG
CYS
9
1_555
A
ZN
32
C
ZN
ZN
1_555
metalc
2.318
A
CYS
12
A
SG
CYS
12
1_555
A
ZN
32
C
ZN
ZN
1_555
metalc
2.411
A
CYS
23
A
SG
CYS
23
1_555
A
ZN
32
C
ZN
ZN
1_555
metalc
2.379
A
CYS
26
A
SG
CYS
26
1_555
A
ZN
32
C
ZN
ZN
1_555
PROTEIN BINDING
Ubiquitin, Protein-Protein complex, Zinc-finger, Rubredoxin knuckle, NZF domain, PROTEIN BINDING
NPL4_RAT
UNP
1
580
Q9ES54
TSAMWACQHCTFMNQPGTGHCEMCSLPRT
UBIQ_HUMAN
UNP
2
1
P62988
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
580
608
1Q5W
3
31
Q9ES54
A
1
3
31
1
76
1Q5W
101
176
P62988
B
2
1
76
1
cloning artifact
GLY
1
1Q5W
A
Q9ES54
UNP
1
1
cloning artifact
SER
2
1Q5W
A
Q9ES54
UNP
2
2
4
anti-parallel
anti-parallel
parallel
anti-parallel
A
TRP
7
A
TRP
7
A
ALA
8
A
ALA
8
A
MET
15
A
MET
15
A
ASN
16
A
ASN
16
B
THR
112
B
THR
12
B
GLU
116
B
GLU
16
B
GLN
102
B
GLN
2
B
THR
107
B
THR
7
B
SER
165
B
SER
65
B
LEU
171
B
LEU
71
B
GLN
141
B
GLN
41
B
ILE
144
B
ILE
44
BINDING SITE FOR RESIDUE ZN A 32
A
ZN
32
Software
4
A
CYS
9
A
CYS
9
4
1_555
A
CYS
12
A
CYS
12
4
1_555
A
CYS
23
A
CYS
23
4
1_555
A
CYS
26
A
CYS
26
4
1_555